Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface

Federation views as a basis for querying and updating database federations

This paper addresses the problem of how to query and update so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. This problem of querying and updating a database federation is tackled by describing a logical architecture and a general semantic framework for precise specification of such database federations, with the aim to provide a basis for implementing a federation by means of relational database views. Our approach to database federations is based on the UML/OCL data model, and aims at the integration of the underlying database schemas of the component legacy systems to a separate, newly defined integrated database schema. One of the central notions in database modelling and in constraint specifications is the notion of a database view, which closely corresponds to the notion of derived class in UML. We will employ OCL (version 2.0) and the notion of derived class as a means to treat (inter-)database constraints and database views in a federated context. Our approach to coupling component databases into a global, integrated system is based on mediation. The first objective of our paper is to demonstrate that our particular mediating system integrates component schemas without loss of constraint information. The second objective is to show that the concept of relational database view provides a sound basis for actual implementation of database federations, both for querying and updating purposes.

The business process modelling ontology

In this paper we describe the Business Process Modelling Ontology (BPMO), which is part of an approach to modelling business processes at the semantic level, integrating knowledge about the organisational context, workflow activities and Semantic Web Services. We harness knowledge representation and reasoning techniques so that business process workflows can: be exposed and shared through semantic descriptions; refer to semantically annotated data and services; incorporate heterogeneous data though semantic mappings; and be queried using a reasoner or inference engine. In this paper we describe our approach and evaluate BPMO through a use case

A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain

Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools

An Architecture for Provenance Systems

This document covers the logical and process architectures of provenance systems. The logical architecture identifies key roles and their interactions, whereas the process architecture discusses distribution and security. A fundamental aspect of our presentation is its technology-independent nature, which makes it reusable: the principles that are exposed in this document may be applied to different technologies

Architecture for Provenance Systems

This document covers the logical and process architectures of provenance systems. The logical architecture identifies key roles and their interactions, whereas the process architecture discusses distribution and security. A fundamental aspect of our presentation is its technology-independent nature, which makes it reusable: the principles that are exposed in this document may be applied to different technologies

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft